I wrote a small Java program that uses the open source Datawarrior library. This program converts the smiles of the drug benazepril into a MOL file. I used the smiles from Pubchem. The generated MOL has only one stereo center instead of two. I have attached the MOL output and the java code to this post.

I am sorry for answering so late. My intention is to answer within 24 hours after being aware of a question. If you don't get a quick answer, you may assume, that I simply didn't see your question (as in this case). Then please send me an e-mail...

I checked your source code, which seem perfectly correct. With the current SmilesParser it also works fine. The problem is
that Smiles were not used at Actelion and therefore I didn't notice that the stereo recognition was not working well.
Recently, we published a paper and a website with structure search on all Wikipedia structures. Since this requires parsing
the Smiles strings from the Wikipedia database, I enhanced the SmilesParser and fixed lots of stereochemistry related and other
issues. You can find the up-to-date version on GitHub in the OpenChemLib project. It will also arrive as part of the
source code of the upcoming new DataWarrior release in hopefully early June.

This is indeed a little tricky. But it is a problem of the CoordinateInventor and not of the SmilesParser.
Generating coordinates is a never ending story. Paul Labute has once written a nice paper about it...